I think I already explained all of that above. Enter as your ordinary traditional IRA contribution the amount that was ineligible for rollover. The rollover reported on your tax return is to reflect only the amount that was eligible for rollover. The excess contribution to the 401(k) and it's attributable earnings is the portion that was not eligible for rollover. If you do substitute Forms 1099-R these will require an explanation statement and the tax return will need to be printed and mailed, so hopefully the 401(k) plan will provide you with Forms 1099-R that correctly reflect the distribution of the excess.
